Publications

growth inhibition by metabolites of gamma-hexachlorocyclohexane in sphingobium japonicum ut26.	the growth of a gamma-hexachlorocyclohexane (gamma-hch)-degrading bacterium sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 in rich medium was inhibited by gamma-hch. this growth inhibition was not observed in a mutant that lacked the initial or second step enzymatic activity for gamma-hch degradation, suggesting that metabolites of gamma-hch are toxic to ut26. two metabolites of gamma-hch, 2,5-dichlorophenol (2,5-dcp) and 2,5-dichlorohydroquinone (2,5-dchq), showed a direct toxi ...	2006	16636477
plasmid pcar3 contains multiple gene sets involved in the conversion of carbazole to anthranilate.	the carbazole degradative car-i gene cluster (caraaibaibbiciaci) of sphingomonas sp. strain ka1 is located on the 254-kb circular plasmid pcar3. carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (cardo; caraaiaci), meta-cleavage enzyme (carbaibbi), and hydrolase (carci). cardo is a three-component dioxygenase, and caraai and caraci are its terminal oxygenase and ferredoxin components. the car-i gene cluster lacks the gene encoding the ferredoxin reductase component ...	2006	16672458
sphingomonas dokdonensis sp. nov., isolated from soil.	a gram-negative, rod-shaped, sphingomonas-like bacterial strain, ds-4(t), was isolated from soil of dokdo, korea, and its taxonomic position was investigated using a polyphasic approach. strain ds-4(t) grew optimally on trypticase soy agar medium without nacl at ph 6.0-6.5 and 25 degrees c. it contained q-10 as the predominant ubiquinone and c(18 : 1)omega7c, c(16 : 0), c(14 : 0) 2-oh and c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh as the major fatty acids. sphingoglycolipid, phosphatidylcholine, ...	2006	16957115
statistical approach to optimization of fermentative production of gellan gum from sphingomonas paucimobilis atcc 31461.	gellan gum, a high-molecular-weight anionic linear polysaccharide produced by pure-culture fermentation from sphingomonas paucimobilis atcc 31461, has elicited industrial interest in recent years as a high-viscosity biogum, a suspending agent, a gelling agent, and an agar substitute in microbial media. in this paper we report on the optimization of gellan gum production using a statistical approach. in the first step, the one factor-at-a-time method was used to investigate the effect of medium c ...	2006	17046526
purification and characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols.	initial reactions involved in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs) include a ring-dihydroxylation catalyzed by a dioxygenase and a subsequent oxidation of the dihydrodiol products by a dehydrogenase. in this study, the dihydrodiol dehydrogenase from the pah-degrading sphingomonas strain chy-1 has been characterized. the bphb gene encoding pah dihydrodiol dehydrogenase (pddh) was cloned and overexpressed as a his-tagged protein. the recombinant protein was purified ...	2006	16820465
characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons.	in sphingomonas chy-1, a single ring-hydroxylating dioxygenase is responsible for the initial attack of a range of polycyclic aromatic hydrocarbons (pahs) composed of up to five rings. the components of this enzyme were separately purified and characterized. the oxygenase component (ht-phni) was shown to contain one rieske-type [2fe-2s] cluster and one mononuclear fe center per alpha subunit, based on epr measurements and iron assay. steady-state kinetic measurements revealed that the enzyme had ...	2006	17014090
sphingomonas soli sp. nov., a beta-glucosidase-producing bacterium in the family sphingomonadaceae in the alpha-4 subgroup of the proteobacteria.	strain t5-04t, a gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in south korea and characterized in order to determine its taxonomic position. 16s rrna gene sequence analysis revealed that strain t5-04t belongs to the alpha-4 subgroup of the proteobacteria, and the highest degrees of sequence similarity determined were to sphingomonas asaccharolytica ifo 10564t (97.5 %), sphingomonas koreensis jss26t (97.1 %), sphingomonas mali ifo 15500t (96.7 ...	2006	16585680
bioremediation of halogenated compounds: comparison of dehalogenating bacteria and improvement of catalyst stability.	five bacterial strains were compared for halogenated compounds conversion in aqueous media. depending on the strain, the optimal temperature for dehalogenase activity of resting cells varied from 30 to 45 degrees c, while optimal ph raised from 8.4 to 9.0. the most effective dehalogenase activity for 1-chlorobutane conversion was detected with rhodococcus erythropolis ncimb13064 and escherichia coli bl21 (de3) (dhaa). the presence of 2-chlorobutane or propanal in the aqueous media could inhibit ...	2006	16723151
cloning, expression, and characterization of a self-sufficient cytochrome p450 monooxygenase from rhodococcus ruber dsm 44319.	a new member of class iv of cytochrome p450 monooxygenases was identified in rhodococcus ruber strain dsm 44319. as the genome of r. ruber has not been sequenced, a p450-like gene fragment was amplified using degenerated primers. the flanking regions of the p450-like dna fragment were identified by directional genome walking using polymerase chain reaction. the primary protein structure suggests a natural self-sufficient fusion protein consisting of ferredoxin, flavin-containing reductase, and p ...	2006	16607529
identification and functional analysis of the genes for naphthalenesulfonate catabolism by sphingomonas xenophaga bn6.	sphingomonas xenophaga bn6 degrades various (substituted) naphthalenesulfonates to the corresponding (substituted) salicylates. a gene cluster was identified on the plasmid pbn6 which coded for several enzymes participating in the degradative pathway for naphthalenesulfonates. a dna fragment of 16 915 bp was sequenced which contained 17 orfs. the genes encoding the 1,2-dihydroxynaphthalene dioxygenase, 2-hydroxychromene-2-carboxylate isomerase, and 2'-hydroxybenzalpyruvate aldolase of the naphth ...	2006	16804169
cutting edge: impaired glycosphingolipid trafficking and nkt cell development in mice lacking niemann-pick type c1 protein.	niemann-pick type c1 (npc1) is a late endosomal/lysosomal transmembrane protein involved in the cellular transport of glycosphingolipids and cholesterol that is mutated in a majority of patients with niemann-pick c neurodegenerative disease. we found that npc1-deficient mice lacked valpha14-jalpha18 nkt cells, a major population of cd1d-restricted t cells that is conserved in humans. npc1-deficient mice also exhibited marked defects in the presentation of sphingomonas cell wall ags to nkt cells ...	2006	16785493
bacterial community in ancient siberian permafrost as characterized by culture and culture-independent methods.	the microbial composition of ancient permafrost sediments from the kolyma lowland of northeast eurasia was examined through culture and culture-independent approaches. these sediments have been continuously frozen for 5,000 to 2-3 million years. a total of 265 bacteria 16s rrna gene sequences were amplified from the permafrost total-community genomic dna and screened by amplified ribosomal 16s rrna restriction analysis. members of three major lineages were found: gamma-proteobacteria (mostly xan ...	2006	16805696
characterization of novel carbazole catabolism genes from gram-positive carbazole degrader nocardioides aromaticivorans ic177.	nocardioides aromaticivorans ic177 is a gram-positive carbazole degrader. the genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. the car genes were clustered into the caraacbabbacad and cardfe gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme a, respectively. th ...	2006	16672473
removal of cyanobacteria, cyanotoxins, heterotrophic bacteria and endotoxins at an operating surface water treatment plant.	the removal of cyanobacteria, hepatotoxins produced by them (microcystins), phytoplankton, heterotrophic bacteria and endotoxins were monitored at a surface water treatment plant with coagulation, clarification, sand filtration, ozonation, slow sand filtration and chlorination as the treatment process. coagulation-sand filtration reduced microcystins by 1.2-2.4, and endotoxins by 0.72-2.01 log10 units. ozonation effectively removed the residual microcystins. the treatment process reduced phytopl ...	2006	17037128
modeling for gellan gum production by sphingomonas paucimobilis atcc 31461 in a simplified medium.	gellan gum production was carried out by sphingomonas paucimobilis atcc 31461 in a simplified medium with a short incubation time, and a kinetic model for understanding, controlling, and optimizing the fermentation process was proposed. the results revealed that glucose was the best carbon source and that the optimal concentration was 30 g liter(-1). as for the fermenting parameters, considerably large amounts of gellan gum were yielded by an 8-h-old culture and a 4% inoculum at 200 rpm on a rot ...	2006	16672479
bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils.	soils contaminated with mineral oil hydrocarbons are often cleaned in off-site bioremediation systems. in order to find out which bacteria are active during the degradation phase in such systems, the diversity of the active microflora in a degrading soil remediation system was investigated by small-subunit (ssu) rrna analysis. two sequential rna extracts from one soil sample were generated by a procedure incorporating bead beating. both extracts were analysed separately by generating individual ...	2006	17074900
microbial degradation of nonylphenol and other alkylphenols--our evolving view.	because the endocrine disrupting effects of nonylphenol (np) and octylphenol became evident, the degradation of long-chain alkylphenols (ap) by microorganisms was intensively studied. most np-degrading bacteria belong to the sphingomonads and closely related genera, while np metabolism is not restricted to defined fungal taxa. growth on np and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. while both bacterial and fungal d ...	2006	16826376
description of sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of sphingomonas cloacae as sphingobium cloacae comb. nov.	a phenanthrene-degrading bacterium, strain tkp(t), was isolated from a fly ash dumping site of the thermal power plant in panki, kanpur, india, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. phylogenetic analysis based on 16s rrna gene sequences indicated that the strain belonged to the genus sphingobium, as it showed highest sequence similarity to sphingobium herbicidovorans dsm 11019(t) (97.3 %) and sphingomonas cloacae jcm 10874(t) (96.5 %), compar ...	2006	16957112
novel upper meta-pathway extradiol dioxygenase gene diversity in polluted soil.	for the determination of the catabolic community diversity that is related to biodegradation potential, we developed a protocol for the assessment of catabolic marker genes in polluted soils. primers specific to upper pathway extradiol dioxygenase genes were designed which amplified a 469-bp product from sphingomonas sp. hv3. the constructed primers were used in pcr amplification of upper pathway ring cleavage genes from dna directly isolated from a mineral oil polluted landfill site, a mineral ...	2006	16958914
multisubstrate biodegradation kinetics for binary and complex mixtures of polycyclic aromatic hydrocarbons.	biodegradation kinetics were studied for binary and complex mixtures of nine polycyclic aromatic hydrocarbons (pahs): naphthalene, 1-methylnaphthalene, 2-methylnaphthalene, 2-ethylnaphthalene, phenanthrene, anthracene, pyrene, fluorene, and fluoranthene. discrepancies between the observed biodegradation rates and those predicted by a sole-substrate model indicate that significant substrate interactions occurred in both the binary and complex-mixture experiments. for all compounds except naphthal ...	2006	16833134
removal and biodegradation of polycyclic aromatic hydrocarbons by selenastrum capricornutum.	the removal and degradation of a mixture of polycyclic aromatic hydrocarbons (pahs), namely phenanthrene (phe), fluoranthene (fla), and pyrene (pyr), by a green microalgal species, selenastrum capricornutum, at different initial cell densities were studied. the pah removal efficiency increased with the initial cell density, and 96% of phe, 100% of fla, and 100% of pyr in the medium were removed by live s. capricornutum at the density of 1 x 10(7) cells/ml in 4 d, whereas less than 50% of pahs we ...	2006	16833137
engineering a beta-carotene ketolase for astaxanthin production.	a new beta-carotene ketolase gene (crtw) was cloned from an environmental isolate sphingomonas sp. dc18. a robust and reliable color screen was developed for protein engineering to improve its activity on hydroxylated carotenoids for astaxanthin production. localized random mutagenesis was performed on the crtw gene including the upstream ribosomal binding site (rbs). six mutations (h96l, r203w, a205v, a208v, f213l and a215t) in the crtw gene were isolated multiple times that showed improved ast ...	2006	16890469
degradability of dimethyl terephthalate by variovorax paradoxus t4 and sphingomonas yanoikuyae dos01 isolated from deep-ocean sediments.	two strains of bacteria were isolated from deep-ocean sediments of the south china sea using enrichment culturing technique and they were identified as sphingomonas yanoikuyae dos01 (ay878409) and variovorax paradoxus t4 (ay878410) based on 16s rrna gene sequences. s. yanoikuyae dos01 was only capable of transforming dimethyl terephthalate (dmtp) to monomethyl terephthalate (mmtp) without further degradation while v. paradoxus t4 exhibited ability in mineralizing dmtp as the sole source of carbo ...	2006	16955363
effects of a small electric current on sterilization of a dental unit water line.	in the present study, water was circulated in a simulated dental unit water line with electrifying a small current. the morphology of the biofilm developed on inner surface of the water line and the number of heterotrophic bacteria were investigated to elucidate the effect of a low level electric current on the biofilms formation associated with bacteria reproduction. destruction and malconformation of biofilms by electrification was observed using sem, in addition to deformation and hypertrophy ...	2006	16913572
identification and quantification of uncultivated proteobacteria associated with pyrene degradation in a bioreactor treating pah-contaminated soil.	uncultivated bacteria associated with the degradation of pyrene in a bioreactor treating soil contaminated with polycyclic aromatic hydrocarbons (pah) were identified by dna-based stable-isotope probing (sip) and quantified by real-time quantitative pcr. most of the 16s rrna gene sequences recovered from (13)c-enriched dna fractions clustered phylogenetically within three separate groups of beta- and gamma-proteobacteria unassociated with described genera and were designated "pyrene groups 1, 2 ...	2006	16958754
[presence of the microbiological risk in umbrian sawmills].	the purpose of this study was to quantify and identify the airborne microbial contamination in umbria sawmills. in this paper we reported the preliminary results of our analysis. microbial contaminants (fungi and bacteria) were assessed with passive (ima standard) and active (sas microbial sampler) methods. there were significant differences of bacterial and/or fungal cfu/m3 values between the outdoor and indoor environments during the normal sawmills activity. staphylococcus, sphingomonas, past ...	2006	17380948
production and rheological characterization of biopolymer of sphingomonas capsulata atcc 14666 using conventional and industrial media.	this work was aimed at the production and rheological characterization of biopolymer by sphingomonas capsulata atcc 14666, using conventional and industrial media. the productivity reached the maximum of 0.038 g/l x h, at 208 rpm and 4% (w/v) of sucrose. for this condition, different concentrations of industrial medium were tested (2.66, 4, 6, and 8%). the best productivity was obtained using pretreated molasses 8% (w/v) (0.296 g/l x h), residue of textured soybean protein 6% (wt/v) (0.244 g/l x ...	2006	16915702
cloning, expression, purification, crystallization and preliminary structure determination of glucose-1-phosphate uridylyltransferase (ugpg) from sphingomonas elodea atcc 31461 bound to glucose-1-phosphate.	the cloning, expression, purification, crystallization and preliminary crystallographic analysis of glucose-1-phosphate uridylyltransferase (ugpg) from sphingomonas elodea atcc 31461 bound to glucose-1-phosphate are reported. diffraction data sets were obtained from seven crystal forms in five different space groups, with highest resolutions ranging from 4.20 to 2.65 a. the phase problem was solved for a p2(1) crystal form using multiple isomorphous replacement with anomalous scattering from an ...	2006	16946483
linear 3-hydroxybutyrate tetramer (hb4) produced by sphingomonas sp. is characterized as a growth promoting factor for some rhizomicrofloral composers.	sphingomonas spp. of alpha-proteobacteria often play a role in assisting the development of microfloral communities under adverse soil conditions. using a frateuria sp. as an indicator for bacterial growth assay, we investigated the bacterial growth-promoting factor in the culture fluids of sphingomonas sp. ec-k085. this factor was successfully isolated and identified as linear (r,r,r,r)-3-hydroxybutyrate tetramer (hb4), having a hydroxy-end and a carboxy-end group. when 28 mug of hb4 was charge ...	2006	16960351
directed evolution of a non-heme-iron-dependent extradiol catechol dioxygenase: identification of mutants with intradiol oxidative cleavage activity.	the non-heme-iron(ii)-dependent extradiol catechol dioxygenases catalyse the oxidative cleavage of substituted catechols found on bacterial aromatic degradation pathways. the reaction mechanism of the extradiol dioxygenases is believed to proceed through the same proximal hydroperoxide intermediate as the iron(iii)-dependent intradiol catechol dioxygenases. directed evolution was carried out on members of the class iii extradiol catechol dioxygenases, by using 1) error-prone polymerase chain rea ...	2006	17051653
blooms of single bacterial species in a coastal lagoon of the southwestern atlantic ocean.	we investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern atlantic ocean. alphaproteobacteria formed the dominant microbial group in both zones throughout the sampling period. after an intrusion of marine water, members of the sar11 lineage became abundant in the brackish-water zone. these bacteria were apparently distributed ove ...	2006	17021206
[construction of double-labelled carbofuran-degrading bacterium sphingomonas sp. cds-1].	the genomic dna of a carbofuran-degrading bacterium sphingomonas sp. cds-1 was digested by sau3al and ligated to probe-gfp digested by bamhi, and the product was transformed to the e. coli dh5alpha competent cells. fifty positive clones that could emit green fluorescence under uv were selected from about 1 x 10(4) clones grown on selective plates amplb. one clone f7 with the strongest fluorescence was selected, the recombinant plasmid pf7 from this clone was digested with ecor i & hind iii and t ...	2006	17037065
proposal to reclassify [sphingomonas] xenophaga stolz et al. 2000 and [sphingomonas] taejonensis lee et al. 2001 as sphingobium xenophagum comb. nov. and sphingopyxis taejonensis comb. nov., respectively.	the sphingomonad group contains bacterial isolates that are quite diverse in terms of their phylogenetic, ecological and physiological properties. thus, the genus sphingomonas was divided into four distinct genera, sphingomonas sensu stricto, sphingobium, novosphingobium and sphingopyxis on the basis of 16s rrna gene sequence phylogenetic analysis, signature nucleotides, fatty acid profiles and polyamine patterns and this classification is currently widely accepted. in this study, a complete ana ...	2006	16514047
molecular diversity studies of bacterial communities of oil polluted microbial mats from the etang de berre (france).	the biodiversity of microbial mats inhabiting the oil-contaminated lagoon etang de berre was determined by molecular approaches. the fingerprint of denaturing gradient gel electrophoresis (dgge) and automatic ribosomal intergenic spacer analysis (arisa) of mats exposed to different pollution levels showed specific microbial communities for each site but similar diversity richness. species composition of the mats were compared by constructing 16s rrna libraries. amplified rdna restriction analysi ...	2006	17117996
[analysis of the degrading products of carbofuran by sphingomonas sp. with gc/ms and gc/ftir].	in different degrading phases, the degrading products of carbofuran by cds-1(sphingomonas sp. ) were extracted by acetone. according to the analysis of gas chromatography/mass spectrometry (gc/ms), carbofuran-7-phenol was identified as the initial degrading product, and an unknown metabolite with molecular weight of 182 was determined as 2-hydroxyl-3-tertiarybutylalcohol-phenol, which was the next degrading product of carbofuran-7-phenol. according to the analysis of gc/ms and gas chromatography ...	2006	17112053
characterization of alkylphenol degradation gene cluster in pseudomonas putida mt4 and evidence of oxidation of alkylphenols and alkylcatechols with medium-length alkyl chain.	alkylphenols (aps) are ubiquitous contaminants in aquatic environments and have endocrine disrupting and toxic effects on aquatic organisms. to investigate biodegradation mechanisms of aps, an ap degradation gene cluster was cloned from a butylphenol (bp)-degrading bacterium, pseudomonas putida mt4. the gene cluster consisted of 13 genes named bupba1a2a3a4a5a6cehifg. from the nucleotide sequences, bupa1a2a3a4a5a6 were predicted to encode a multicomponent phenol hydroxylase (ph), whereas bupbcehi ...	2006	17116584
isolation and physiological characterization of the pentachlorophenol degrading bacterium sphingomonas chlorophenolica.	many chlorophenols tend to persist in the environment, and they may become public health hazards. among chlorophenols, pentachlorophenol (pcp) is a priority pollutant that has been used widely as a general biocide in commercial wood treatment. owing to the rapid industrial growth, serious soil and water pollutions by chlorophenols has been reported in taiwan. in this study, 10 indigenous pcp-degrading bacterial strains were isolated from a pcp-degrading mixed culture, and the potential of both t ...	2006	16005492
characterization of four rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols.	four genes were isolated and characterized for alcohol dehydrogenases (adhs) catalyzing the oxidation of aromatic alcohols such as benzyl alcohol to their corresponding aldehydes, one from o-xylene-degrading rhodococcus opacus tkn14 and the other three from n-alkane-degrading rhodococcus erythropolis pr4. various aromatic alcohols were bioconverted to their corresponding carboxylic acids using escherichia coli cells expressing each of the four adh genes together with an aromatic aldehyde dehydro ...	2006	16292529
engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria.	sphingomonas sp. a1 possesses specialized membrane structures termed 'superchannels' that enable the direct incorporation of macromolecules into the cell. we have engineered two related sphingomonads, the dioxin-degrading s. wittichii rw1 and the polypropylene glycol-degrading s. subarctica ifo 16058(t), to incorporate this superchannel into their cell membranes. in both cases the bioremediation capability of the organisms was substantially increased pointing at the potential of this approach as ...	2006	16415854
microbial contamination of nebulization solution and its measures.	we evaluated the microbial contamination of nebulization solutions in medication cups from a total of 76 ultrasonic nebulizers in use in 10 hospitals. in addition, an interview survey was given to nurses to evaluate the disinfection methods of these ultrasonic nebulizers. of a total of 76 nebulization solution samples, 11 (14.5%) were contaminated with 10-10(2) colony-forming units (cfu)/ml and 9 (11.8%) with 10(3)-10(5) cfu/ml. the major contaminants were glucose non-fermentative bacilli such a ...	2006	16508154
effect of sphingobium yanoikuyae b1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly pah-contaminated soils.	sphingobium yanoikuyae b1 is able to degrade a range of polycyclic aromatic hydrocarbons (pahs) and as a sphingomonad belongs to one of the dominant genera found in pah-contaminated soils. we examined the ecological effect that soil inoculation with s. yanoikuyae b1 has on the native bacterial community in three different soils: aged pah-contaminated soil from an industrial site, compost freshly contaminated with pahs and un-contaminated compost. survival of s. yanoikuyae b1 was dependent on the ...	2006	16524654
effect of bioaugmentation and supplementary carbon sources on degradation of polycyclic aromatic hydrocarbons by a soil-derived culture.	the degradation of polycyclic aromatic hydrocarbons (pahs) by an undefined culture obtained from a pah-polluted soil and the same culture bioaugmented with three pah-degrading strains was studied in carbon-limited chemostat cultures. the pahs were degraded efficiently by the soil culture and bioaugmentation did not significantly improve the pah degrading performance. the presence of pahs did, however, influence the bacterial composition of the bioaugmented and non-bioaugmented soil cultures, res ...	2006	16420621
degradation of microcystin-rr by sphingomonas sp. cba4 isolated from san roque reservoir (córdoba - argentina).	we report the aerobic biodegradation of microcystin-rr (mc-rr) by a bacterial strain isolated from san roque reservoir (córdoba - argentina). this bacterium was identified as sphingomonas sp. (cba4) on the basis of 16s rdna sequencing. the isolated strain was capable of degrading completely mc-rr (200 mug l(-1)) within 36 h. we have found evidence that mc-rr biodegradation pathway by this sphingomonas sp. strain would start by demethylating mc-rr, affording an intermediate product, which is fina ...	2006	16485086
bioremediation of hydrocarbon-contaminated polar soils.	bioremediation is increasingly viewed as an appropriate remediation technology for hydrocarbon-contaminated polar soils. as for all soils, the successful application of bioremediation depends on appropriate biodegradative microbes and environmental conditions in situ. laboratory studies have confirmed that hydrocarbon-degrading bacteria typically assigned to the genera rhodococcus, sphingomonas or pseudomonas are present in contaminated polar soils. however, as indicated by the persistence of sp ...	2006	16514512
sequence and analysis of the 46.6-kb plasmid pa1 from sphingomonas sp. a1 that corresponds to the typical incp-1beta plasmid backbone without any accessory gene.	sphingomonas sp. a1 (strain a1) is capable of directly incorporating macromolecules (e.g., alginate) through the specialized import system--"super-channel." here, we report the complete dna sequence and genetic organization of plasmid pa1 from strain a1. nucleotide sequence analysis revealed that pa1 comprises 46,557 bp encoding 49 open reading frames (orfs) with 65% g+c content and abundant gccg/cggc motifs. many predicted pa1 orfs showed high similarity to pa81 orfs; pa81 is supposedly a self- ...	2006	16445980
distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in sphingobium japonicum ut26.	sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 utilizes the important insecticide gamma-hexachlorocyclohexane as a sole source of carbon and energy. in previous studies, we isolated and characterized six structural genes (lina to linf) and one regulatory gene (linr) of ut26 for the degradation of gamma-hexachlorocyclohexane to beta-ketoadipate. our analysis in this study indicated that the ut26 genome consists of three large circular replicons of 3.6 mb, 670 kb, and 185 kb. the ...	2006	16487327
biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p- dioxin by sphingomonas wittichii strain rw1.	sphingomonas wittichii rw1 is able to catabolize 1,2,3,4-tetrachlorodibenzo-p-dioxin (h. b. hong, y. s. chang, i. h. nam, p. fortnagel, and s. schmidt, appl. environ. microbiol. 68:2584-2588, 2002). here we demonstrate the aerobic bacterial catabolism of the ubiquitous toxic diaryl ether pollutant 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by this strain. the products of this biotransformation were identified as tetrachlorocatechol and 2-methoxy-3,4,5,6-tetrachlorophenol by comparing mass spectra re ...	2006	16391032
the degradation of alpha-quaternary nonylphenol isomers by sphingomonas sp. strain ttnp3 involves a type ii ipso-substitution mechanism.	the degradation of radiolabeled 4(3',5'-dimethyl-3'-heptyl)-phenol [nonylphenol (np)] was tested with resting cells of sphingomonas sp. strain ttnp3. concomitantly to the degradation of np, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. two other radiolabeled isomers of np, 4(2',6'-dimethyl-2'-heptyl)-phenol and 4(3',6'-dimethyl-3'-heptyl)-phenol, were synthesized. in parallel experiments, the 4(2', ...	2006	16091931
expression of glycosylated haloalkane dehalogenase linb in pichia pastoris.	heterologous expression of the bacterial enzyme haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 in methylotrophic yeast pichia pastoris is reported. the haloalkane dehalogenase gene linb was subcloned into the ppiczalphaa vector and integrated into the genome of p. pastoris. the recombinant linb secreted from the yeast was purified to homogeneity and biochemically characterized. the deglycosylation experiment and mass spectrometry measurements showed that the recombinant linb ex ...	2006	16216524
molecular microbial diversity of a soil sample and detection of ammonia oxidizers from cape evans, mcmurdo dry valley, antarctica.	the aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, cape evans, mcmurdo, antarctica by an ssu rdna gene library approach. our study by sequencing of clones from ssu rdna gene library approach revealed high diversity in the soil sample from antarctica. more than 50% of clones showed homology to cytophaga-flavobacterium-bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, thermus-deinococcus and high gc ...	2007	16517136
papaya shoot tip associated endophytic bacteria isolated from in vitro cultures and host-endophyte interaction in vitro and in vivo.	fourteen distinct bacterial clones were isolated from surface-sterilized shoot tips (approximately 1 cm) of papaya (carica papaya l. 'surya') planted on murashige and skoog (ms)-based papaya culture medium (23/50 nos.) during the 2-4 week period following in vitro culturing. these isolates were ascribed to six gram-negative genera, namely pantoea (p. ananatis), enterobacter (e. cloacae), brevundimonas (b. aurantiaca), sphingomonas, methylobacterium (m. rhodesianum), and agrobacterium (a. tumefac ...	2007	17538647
investigation of microbial communities on reverse osmosis membranes used for process water production.	in the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (ro) membranes were determined. fresh surface water was used as a feed in a membrane-based water purification process. total dna was extracted from attached cells from feed spacer, ro membrane and product spacer. universal primers were used to amplify the bacterial 16s rrna genes. the biofilm community was analysed by 16s rrna-gene-targeted denaturing gradient gel electrophor ...	2007	17546985
measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions.	substrate depletion experiments were conducted to characterize aerobic biodegradation of 20 single polycyclic aromatic hydrocarbons (pahs) by induced sphingomonas paucimobilis strain epa505 in liquid suspensions. pahs consisted of low molecular weight, unsubstituted, and methyl-substituted homologs. a material balance equation containing the andrews kinetic model, an extension of the monod model accounting for substrate inhibition, was numerically fitted to batch depletion data to estimate extan ...	2007	17115446
kinetics of biodegradation of binary and ternary mixtures of pahs.	the kinetics of biodegradation of mixtures of polycyclic aromatic hydrocarbons (pahs) by sphingomonas paucimobilis strain epa505 were investigated. the investigation focused on three- and four-ring pahs, specifically 2-methylphenanthrene, fluoranthene, and pyrene. uptake rates in aerobic batch suspended cultivations were measured for the individual pahs and their binary and ternary mixtures. it was observed that kinetics were influenced by the mixture composition and the kinetic properties of th ...	2007	17115447
sphingomonas mucosissima sp. nov. and sphingomonas desiccabilis sp. nov., from biological soil crusts in the colorado plateau, usa.	two bacterial strains, cp173-2(t) and cp1d(t), were isolated from biological soil crusts (bscs) collected in the colorado plateau, usa. both strains were pigmented, gram-negative, non-motile rods and produced abundant mucus. they contained c(16 : 0), c(18 : 1)omega7c and c(14 : 0) 2-oh as the predominant cellular fatty acids, ubiquinone-10 as the isoprenoid quinone and sphingoglycolipid. based on the above characteristics, the isolates were assigned to the family sphingomonadaceae; 16 rrna gene ...	2007	17473253
elucidation of the ipso-substitution mechanism for side-chain cleavage of alpha-quaternary 4-nonylphenols and 4-t-butoxyphenol in sphingobium xenophagum bayram.	recently we showed that degradation of several nonylphenol isomers with alpha-quaternary carbon atoms is initiated by ipso-hydroxylation in sphingobium xenophagum bayram (f. l. p. gabriel, a. heidlberger, d. rentsch, w. giger, k. guenther, and h.-p. e. kohler, j. biol. chem. 280:15526-15533, 2005). here, we demonstrate with 18o-labeling experiments that the ipso-hydroxy group was derived from molecular oxygen and that, in the major pathway for cleavage of the alkyl moiety, the resulting nonanol ...	2007	17369338
isolation and identification of a novel microcystin-degrading bacterium from a biological sand filter.	a novel bacterium capable of degrading two microcystin analogues, microcystin-lr and -la (mclr and mcla), was isolated from a biological sand filter which was previously shown to effectively remove these toxins from source waters. based on phylogenetic analysis of the 16s rrna gene sequence, the isolated organism, lh21, most likely belonged to the genus sphingopyxis and of the previously cultured species clustered with sphingopyxis witflariensis. using polymerase chain reaction (pcr), isolate lh ...	2007	17640697
biofilm interactions between distinct bacterial genera isolated from drinking water.	in the environment, multiple microorganisms coexist as communities, competing for resources and often associated as biofilms. in this study, single- and dual-species biofilm formation by, and specific activities of, six heterotrophic intergeneric bacteria were determined using 96-well polystyrene plates over a 72-h period. these bacteria were isolated from drinking water and identified by partial 16s rrna gene sequencing. a series of planktonic studies was also performed, assessing the bacterial ...	2007	17675433
combination enzyme therapy for gastric digestion of dietary gluten in patients with celiac sprue.	celiac sprue is a multifactorial disease characterized by an inflammatory response to ingested gluten in the small intestine. proteolytically resistant, proline- and glutamine-rich gluten peptides from wheat, rye, and barley persist in the intestinal lumen and elicit an immune response in genetically susceptible persons. we investigated a new combination enzyme product, consisting of a glutamine-specific endoprotease (ep-b2 from barley) and a prolyl endopeptidase (sc pep from sphingomonas capsul ...	2007	17681168
sphingomonas fennica sp. nov. and sphingomonas haloaromaticamans sp. nov., outliers of the genus sphingomonas.	bacterial isolates obtained from polychlorophenol-contaminated sites in finland (strain k101(t)) and from a dutch drinking water well (strain a175(t)) were characterized taxonomically. 16s rrna gene sequence analysis, determination of dna g+c content, physiological characterization, estimation of the ubiquinone and polar lipid patterns and fatty acid content revealed that strains k101(t) and a175(t) were similar to sphingomonas wittichii rw1(t) but also showed pronounced differences. the dna g+c ...	2007	17684248
chlorophenol hydroxylase activity encoded by tfdb from 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading bradyrhizobium sp. strain rd5-c2.	the tfdb gene encoding chlorophenol hydroxylase and its homolog were found in 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading strain rd5-c2, which belongs to bradyrhizobium sp. of alpha-proteobacteria. the nucleotide and deduced amino acid sequence identities of the two genes, designated tfdba and tfdbb, were 60% and 57% respectively. their nucleotide sequences most closely matched those of previously reported tfdb, which consisted of those from 2,4-d-degrading beta- and gamma-proteobacteria an ...	2007	17617713
sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.	an aerobic, gram-negative, yellow-pigmented, non-motile bacterium, designated strain kmm 3882t, was isolated from a marine bivalve (anadara broughtoni) collected from peter the great bay, sea of japan, and was subjected to phenotypic and phylogenetic analyses. strain kmm 3882t was found to exert a remarkable inhibitory activity against a number of gram-positive micro-organisms. phylogenetic analysis based on 16s rrna gene sequences placed strain kmm 3882t within the genus sphingomonas, as an ind ...	2007	17267979
microbial aspects of the interaction between soil depth and biodegradation of the herbicide isoproturon.	factors controlling change in biodegradation rate of the pesticide isoproturon with soil depth were investigated in a field with sandy-loam soil. soil was sampled at five depths between 0-10 and 70-80 cm. degradation rate declined progressively down the soil profile, with degradation slower, and relative differences in degradation rate between soil depths greater, in intact cores relative to sieved soil. neither the maximum rate of degradation, or sorption, changed with soil depth, indicating th ...	2007	16996107
cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading sphingomonas sp. strain.	a carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. the isolate, designated sphingomonas sp. strain xldn2-5, could utilize carbazole (ca) as the sole source of carbon, nitrogen, and energy. washed cells of strain xldn2-5 were shown to be capable of degrading dibenzofuran (dbf) and dibenzothiophene (dbt). examination of metabolites suggested that xldn2-5 degraded dbf to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic a ...	2007	17337542
culturable leaf-associated bacteria on tomato plants and their potential as biological control agents.	culturable leaf-associated bacteria inhabiting a plant have been considered as promising biological control agent (bca) candidates because they can survive on the plant. we investigated the relationship between bacterial groups of culturable leaf-associated bacteria on greenhouse- and field-grown tomato leaves and their antifungal activities against tomato diseases in vitro and in vivo. in addition, the isolated bacteria were analyzed for n-acyl-homoserine lactone (ahl) and indole-3-acetic acid ...	2007	17356949
simultaneous biodegradation of methyl parathion and carbofuran by a genetically engineered microorganism constructed by mini-tn5 transposon.	a genetically engineered microorganism (gem) capable of simultaneous degrading methyl parathion (mp) and carbofuran was successfully constructed by random insertion of a methyl parathion hydrolase gene (mpd) into the chromosome of a carbofuran degrading sphingomonas sp. cds-1 with the mini-transposon system. the gem constructed was relatively stable and cell viability and original degrading characteristic was not affected compared with the original recipient cds-1. the effects of temperature, in ...	2007	17091349
novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates.	the microbial community and sulfur oxygenase reductases of metagenomic dna from bioreactors treating gold-bearing concentrates were studied by 16s rrna library, real-time polymerase chain reaction (rt-pcr), conventional cultivation, and molecular cloning. results indicated that major bacterial species were belonging to the genera acidithiobacillus, leptospirillum, sulfobacillus, and sphingomonas, accounting for 6.3, 66.7, 18.8, and 8.3%, respectively; the sole archaeal species was ferroplasma sp ...	2007	17111141
influence of solution ionic strength on the collision efficiency distribution and predicted transport distance of a sphingomonas sp. flowing through porous media.	the effects of solution ionic strength on the collision efficiency (alpha) distribution of a sphingomonas sp. were investigated using multiple sand columns of varying lengths and analyzing the bacteria clean-bed breakthrough concentrations using a distributed colloid filtration theory (d-cft). five different probability density functions (pdfs) were investigated and all accurately replicated the lab-scale experimental data, whereas a single alpha value could not. the alpha distribution shifted t ...	2007	17644150
cell surface structure enhancing uptake of polyvinyl alcohol (pva) is induced by pva in the pva-utilizing sphingopyxis sp. strain 113p3.	polyvinyl alcohol (pva)-utilizing sphingopyxis sp. 113p3 (re-identified from sphingomonas sp. 113p3) removed almost 0.5% pva from culture supernatants in 4 days. faster degradation of 0.5% pva was performed by the periplasmic fraction. the average molecular size of pva in the culture supernatant or cell-bound pva was gradually shifted higher, suggesting that lower molecular size molecules are degraded faster. depolymerized products were found in neither the culture supernatant nor the cell-bound ...	2007	17453173
bacterial contamination of water in dental unit reservoirs.	the aim of this study was bacteriological assessment of water in dental unit reservoirs--concentration and composition of the aerobe and facultative anaerobe bacterial microflora. reservoir water samples were taken from 25 units. bacterial flora were determined with the plate culture method. bacteria were identified with biochemical microtests: api 20e, api 20ne (biomérieux, france) and gp2 microplatetm (biolog, usa). the concentration of total bacteria isolated from one site was 201,039 cfu/ml, ...	2007	17655191
role of dissolved humic acids in the biodegradation of a single isomer of nonylphenol by sphingomonas sp.	this study shows the important role of humic acids in the degradation of (14)c and (13)c labeled isomer of np by sphingomonas sp. strain ttnp3 and the detoxification of the resulting metabolites. due to the association of np with humic acids, its solubility in the medium was enhanced and the extent of mineralization of nonylphenol increased from 20% to above 35%. this was accompanied by the formation of significant amounts of np residues bound to the humic acids, which also occurred via abiotic ...	2007	17367841
4-sulfomuconolactone hydrolases from hydrogenophaga intermedia s1 and agrobacterium radiobacter s2.	the 4-carboxymethylen-4-sulfo-but-2-en-olide (4-sulfomuconolactone) hydrolases from hydrogenophaga intermedia strain s1 and agrobacterium radiobacter strain s2 are part of a modified protocatechuate pathway responsible for the degradation of 4-sulfocatechol. in both strains, the hydrolase-encoding genes occur downstream of those encoding the enzymes that catalyze the lactonization of 3-sulfomuconate. the deduced amino acid sequences of the 4-sulfomuconolactone hydrolases demonstrated the highest ...	2007	17660282
the catalytic pocket of the ring-hydroxylating dioxygenase from sphingomonas chy-1.	ring-hydroxylating dioxygenases are multicomponent bacterial enzymes that catalyze the first step in the oxidative degradation of aromatic hydrocarbons. the dioxygenase from sphingomonas chy-1 is unique in that it can oxidize a wide range of polycyclic aromatic hydrocarbons (pahs). with a crystal structure similar to that of the seven other known dioxygenases, its catalytic domain features the largest hydrophobic substrate binding cavity characterized so far. molecular modeling studies indicated ...	2007	17157819
genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds.	lignins are the most abundant aromatic compounds in nature, and their decomposition is essential to the terrestrial carbon cycle. white rot fungi secreting phenol oxidases are assumed to be involved in the initial degradation of native lignin, whereas bacteria play a main role in the mineralization of lignin-derived low-molecular-weight compounds in soil. there are a number of reports on the degradation pathways for lignin-derived aromatic compounds, but their catabolism has not been enzymatical ...	2007	17213657
influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by sphingomonas sp. strain pheb4.	the influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (pahs) was investigated when sphingomonas sp. strain pheb4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (pmsm) or nutrient broth (nb). the nb-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate pahs compared to the pmsm-grown culture. the concentrations of pah metabolites were also lower in nb- ...	2007	17216444
the structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis.	sphingolipid biosynthesis commences with the condensation of l-serine and palmitoyl-coa to produce 3-ketodihydrosphingosine (kds). this reaction is catalysed by the plp-dependent enzyme serine palmitoyltransferase (spt; ec 2.3.1.50), which is a membrane-bound heterodimer (spt1/spt2) in eukaryotes such as humans and yeast and a cytoplasmic homodimer in the gram-negative bacterium sphingomonas paucimobilis. unusually, the outer membrane of s. paucimobilis contains glycosphingolipid (gsl) instead o ...	2007	17559874
changes to the structure of sphingomonas spp. communities associated with biodegradation of the herbicide isoproturon in soil.	the phenyl-urea herbicide isoproturon is a major contaminant of surface and ground-water in agricultural catchments. earlier work suggested that within-field spatial variation of isoproturon degradation rate resulted from interactions between catabolizing sphingomonas spp. and ph. in the current study, changes to the structure of sphingomonas communities during isoproturon catabolism were investigated using sphingomonas-specific 16s rrna gene primers. growth-linked catabolism at high-ph (>7.5) s ...	2007	17241244
parameters controlling the gene-targeting frequency at the sphingomonas species rrn site and expression of the methyl parathion hydrolase gene.	to investigate the key parameters controlling the exogenous methyl parathion hydrolase (mph) gene mpd-targeting frequency at the ribosomal rna operon (rrn) site of sphingomonas species which has a wide range of biotechnological applications.	2007	17578423
bacterial synthesis of poly(hydroxybutyrate- co-hydroxyvalerate) using carbohydrate-rich mahua (madhuca sp.) flowers.	the objective of the present work was to utilize an unrefined natural substrate namely mahua (madhuca sp.) flowers, as a carbon source for the production of bacterial polyhydroxyalkanoate (pha) copolymer by bacillus sp-256.	2007	17584466
bacterial community composition and structure of biofilms developing on nanofiltration membranes applied to wastewater treatment.	the structure and microbial communities of biofilms developing on cross-flow nanofiltration (nf) membranes at different temperatures (20, 25 or 34 degrees c) and operation lengths (8h-24days) were studied. feedwater comprised tertiary quality wastewater effluent or synthetic media mimicking effluents of intermediate quality. after each run, the membranes were autopsied for bacterial enumeration, bacterial community composition and microscopy visualization (sem, clsm and afm/nsom). community comp ...	2007	17585989
identification of an il-17-producing nk1.1(neg) inkt cell population involved in airway neutrophilia.	invariant natural killer t (inkt) cells are an important source of both t helper type 1 (th1) and th2 cytokines, through which they can exert beneficial, as well as deleterious, effects in a variety of inflammatory diseases. this functional heterogeneity raises the question of how far phenotypically distinct subpopulations are responsible for such contrasting activities. in this study, we identify a particular set of inkt cells that lack the nk1.1 marker (nk1.1(neg)) and secrete high amounts of ...	2007	17470641
cyclodextrin-linked alginate beads as supporting materials for sphingomonas cloacae, a nonylphenol degrading bacteria.	calcium alginate beads covalently linked with alpha-cyclodextrin (alpha-cd-alginate beads) were prepared and examined for their ability to serve as a supporting matrix for bacterial degradation of nonylphenol, an endocrine disruptor. column chromatographic experiment using alpha-cd-alginate beads with diameter of 657+/-82 microm and with degree of cd substitution of 0.16 showed a strong affinity for nonylphenol adsorption. although addition of alpha-cd (2.7-27 mm) to the culture broth of sphingo ...	2007	17055261
the complex of sphingomonas elodea atcc 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members.	gellan gum is a widely used commercial material, available in many different forms. its economic importance has led to studies into the biosynthesis of exopolysaccharide gellan gum, which is industrially prepared in high yields using sphingomonas elodea atcc 31461. glucose-1-phosphate uridylyltransferase mediates the reversible conversion of glucose-1-phosphate and utp into udp-glucose and pyrophosphate, which is a key step in the biosynthetic pathway of gellan gums. here we present the x-ray cr ...	2007	17434970
potential of the adhesion of bacteria isolated from drinking water to materials.	heterotrophic bacteria (11 genera, 14 species, 25 putative strains) were isolated from drinking water, identified either biochemically or by partial 16s rdna gene sequencing and their adherence characteristics were determined by two methods: i. thermodynamic prediction of adhesion potential by measuring hydrophobicity (contact angle measurements) and ii. by measuring adherence to eight different substrata (asi 304 and 316 stainless steel, copper, polyvinyl chloride, polypropylene, polyethylene, ...	2007	17440920
deproteinization of gellan gum produced by sphingomonas paucimobilis atcc 31461.	deproteinization is a technical bottleneck in the purification of viscous water-soluble polysaccharides. the aim of this work is to provide an appropriate approach to deproteinize crude gellan gum. several methods of deproteinization were investigated, including sevag method, alkaline protease, papain and neutral protease. the results revealed that sevag method had high deproteinization efficiency (87.9%), but it showed dissatisfactory recovery efficiency of gellan gum (28.6%), which made it les ...	2007	17069918
a gene linb2 responsible for the conversion of beta-hch and 2,3,4,5,6-pentachlorocyclohexanol in sphingomonas sp. bhc-a.	commercial formulations of hexachlorocyclohexane (hch) consist of a mixture of four isomers: alpha, beta, gamma, and delta. all four isomers are toxic and recalcitrant pollutants. beta-hch is more problematic due to its longer persistence in the environment. sphingomonas sp. bhc-a was able to degrade not only alpha-, gamma-, and delta-hch but also beta-hch. to clone a gene responsible for the degradation of beta-hch, a tn5 mutation was introduced into bhc-a, and one mutant bhc-a45 defective in b ...	2007	16977465
diethyl phthalate in compost: ecotoxicological effects and response of the microbial community.	there is a great need to understand the environmental impacts of organic pollutants on soil health. phthalates are widely used in consumables and can be found extensively. we studied the toxicity of diethyl phthalate (dep), spiked in a compost plant growth substrate, by means of the acute toxicity flash test and on the basis of the germination and plant growth of radish seedlings. the response of the microbial community to dep in the growth substrate was studied by pcr-dgge (denaturing gradient ...	2007	17258270
dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment.	the structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. a laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with cu(ii) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. between 73 and 90 % of the cu(ii) was removed from water during long-term operation (over 200 days). ...	2007	17259604
biodegradation rates of 2-methylisoborneol (mib) and geosmin through sand filters and in bioreactors.	taste and odour (t&o) causing compounds, in particular, 2-methylisoborneol (mib) and geosmin, are a problem for water authorities as they are recalcitrant to conventional water treatment. in this study, biological sand filtration was shown to be an effective process for the complete removal of mib and geosmin, with removal shown to be predominantly through biodegradation. in addition, mib and geosmin were also effectively degraded in batch bioreactor experiments using biofilm sourced from one of ...	2007	17005238
design of sphingomonad-detecting probes for a dna array, and its application to investigate the behavior, distribution, and source of rhizospherous sphingomonas and other sphingomonads inhabiting an acid sulfate soil paddock in kalimantan, indonesia.	throughout central and south kalimantan, indonesia, strongly acidic soil (ph 2.1-3.7) is widely distributed, and the local acidic soil-tolerant plants, including local rice varieties, often possess sphingomonads in their rhizosphere and rhizoplane. to investigate the behavior of sphingomonads inhabiting the rhizosphere of such acid-tolerant plants, we designed 13 different dna array probes (each of 72 mer) specific to a group of sphingomonads, using a hypervariable v6 region of the 16s rrna gene ...	2007	17284854
optimisation of the long-term efficacy of dental chair waterline disinfection by the identification and rectification of factors associated with waterline disinfection failure.	although many studies have highlighted the problem of biofilm growth in dental chair unit waterlines (duws), no long-term studies on the efficacy of duw disinfection using a large number of dental chair units (dcus) have been reported.	2007	17303302
isolation of a chlorpyrifos-degrading bacterium, sphingomonas sp. strain dsp-2, and cloning of the mpd gene.	a highly effective chlorpyrifos-degrading bacterium strain dsp-2 was isolated from the polluted treatment system of a chlorpyrifos manufacturer. this strain was preliminarily identified as sphingomonas sp. based on its morphological, physiological and biochemical tests as well as 16s rdna analysis. it utilized chlorpyrifos as its sole source of carbon for growth, by hydrolyzing chlorpyrifos to 3,5,6-trichloro-2-pyridinol (tcp). it could also utilize parathion, parathion-methyl, fenitrothion and ...	2007	17306510
17beta-estradiol-degrading bacteria isolated from activated sludge.	fourteen phylogenetically diverse 17beta-estradiol-degrading bacteria (strains kc1-14) were isolated from activated sludge of a wastewater treatment plant. these isolates widely distributed among eight different genera--aminobacter (strains kc6 and kc7), brevundimonas (strain kc12), escherichia (strain kc13), flavobacterium (strain kc1), microbacterium (strain kc5), nocardioides (strain kc3), rhodococcus (strain kc4), and sphingomonas (strains kc8-kc11 and kc14)--of three phyla: proteobacteria, ...	2007	17310711
plant carbohydrate scavenging through tonb-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria.	tonb-dependent receptors (tbdrs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in gram-negative bacteria. analysis of the genome of the phytopathogenic bacterium xanthomonas campestris pv. campestris (xcc), predicts 72 tbdrs. such an overrepresentation is common in xanthomonas species but is limited to only a small number of bacteria. here, we show that one xcc tbdr transports sucrose with a very high affinity, suggesting that it might be a sucro ...	2007	17311090
molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at vostok, east antarctica.	decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. at the vostok drill site, a total of 3650 m of ice core have now been obtained from the east antarctic ice sheet. the ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. in the present study we used 16s rrna gene sequencing to analyze the bacterial content of the vostok drilling fluid samp ...	2007	17313578
decolorisation and detoxification of direct blue-15 by a bacterial consortium.	studies were carried out on decolorisation and biotransformation of the dye direct blue-15 into 3,3'-dimethoxybenzidine (o'-dianisidine) and a sulphonated derivative by a five-member bacterial consortium. chromatographic studies revealed further complete biodegradation of 3,3'-dimethoxybenzidine coupled with release of ammonia, but the recalcitrant sulphonated derivative persisted. the microorganisms identified in the mixed consortium by 16s rdna sequence analysis were alcaligenes faecalis, sphi ...	2007	17321737
microorganisms isolated from the water phase of tropospheric clouds at the puy de dôme: major groups and growth abilities at low temperatures.	this work constitutes the first large report on aerobic cultivable microorganisms present in cloud water. seven cloud-event samples were collected at the puy de dôme summit, and cultivation was performed leading to the isolation of 71 bacterial, 42 fungal and 15 yeast strains. most of the fungi isolated were of cladosporium or trametes affiliation, and yeasts were of cryptococcus affiliation. bacteria, identified on the basis of their 16s rrna gene sequence, were found to belong to actinobacteri ...	2007	17328765
study of substrate inhibition by electrophoretically mediated microanalysis in partially filled capillary.	substrate inhibition is a common phenomenon in enzyme kinetics. we report here for the first time its study by a combination of the electrophoretically mediated microanalysis (emma) methodology with a partial filling technique. in this setup, the part of capillary is filled with the buffer best for the enzymatic reaction whereas, the rest of the capillary is filled with the background electrolyte optimal for separation of substrates and products. in the case of haloalkane dehalogenase, a model e ...	2007	17010980
structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1.	the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ...	2007	17349044
integrated response to inducers by communication between a catabolic pathway and its regulatory system.	efficient gene regulation of metabolic pathways implies that the profile of molecules inducing the pathway matches that of the molecules that are metabolized. gratuitous induction, a well-known phenomenon in catabolic pathways, is the consequence of differences in the substrate and inducer profiles. this phenomenon is particularly evident in pathways for biodegradation of organic contaminants that can be induced by a variety of molecules similar to the real substrates. analysis of the regulation ...	2007	17351041